Indel detectors for Ion Torrent data

Question

[genya35]

Hello,

Could someone please suggest a good indel detector to use on IonTorrent BWA-Mem aligned bam files. I've tried Pindel and achieved good results, however, some indels are still missed.

Thanks

[cpad0112]

1. Was there a recalibration step with known indels post alignment?
2. You can also try PINDEL derivatives like DINDEL, GINDEL etc. DINDEL takes output from PINDEL.

Answer 1

[Kevin Blighe]

I think that pindel is fine. The issue may relate to the general issues of calling indels from NGS data.

Some things to consider:

• Have you visually look at how the reads have aligned over the regions in which indels were not called? They may be problematic regions, like for example homopolymeric regions. I would load your aligned BAMs into IGV
• Check your mapping quality (MAPQ) filter thresholds (reads with indels will automatically receive lo MAPQ unless we specifically treat them differently
• Consider your indel length in relation to your read length. As you're using Ion Torrent, I guess that your reads are ~75bp? If you are trying to detect indels from reads of this size, it will always be difficult.
• Consider downloading your BAMs from the Torrent Server and then using something like GATK IndelRealigner followed by HaplotypeCaller in order to attempt to identify the indels.